Frequently Asked Questions

Exception in thread "main" java.lang.NoClassDefFoundError: MSFragger/jar
There is a current error in the manual that leaves out the -jar flag. A correct call to run MSFragger is java -Xmx8G -jar MSFragger.jar fragger.params file1.mzML file2.mzML

X!Tandem as the search engine in pepXML output
Peptide validation tools do not currently have support for MSFragger so MSFragger masquerades as X!Tandem for compatibility with tools like PeptideProphet. As the hyperscore calculated by MSFragger is slightly different than that of X!Tandem, this may be suboptimal in certain situations. We hope to change this in the future once there is support for MSFragger in peptide validation tools.

No target sequences to search against
The parameter file is missing. The parameter file must be the first argument to MSFragger

MGF file errors
MGF file support within MSFragger is limited to files generated from Proteowizard. We recommend converting your MGF files to mzML prior to searching with MSFragger